Dan Li

### Description of the bug I installed `nextflow` with `conda install -c bioconda nextflow` on HPC, which has Singularity3.7.1 When I `nextflow -Dcapsule.log=verbose` There is error: ``` CAPSULE: Jar: /lila/home/lid/miniconda3/envs/nf-core/share/nextflow/dist/20.10.0/nextflow-20.10.0-one.jar...

ERROR - Can not locate the barcodes.tsv file! for Cellranger Multiplexing outputs

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The Cellranger Multiplexing outputs has a different folder direction:  The command ``` velocyto run10x -m mm10_rmsk.gtf TCEVdox015-12677-1 gtf/Mus_musculus.GRCm38.93_costom_filtered3.gtf ``` has an error ``` ERROR - Can not locate the...

Hello, Thank you for creating this great tool! I had an error when running `velocyto run10x` function on the cluster: ``` ...... 2021-12-30 00:49:21,224 - DEBUG - 7665458 reads were...

Hi, ``` import imageio reader = imageio.get_reader('../data/p1ch4/video-cockatoo/cockatoo.mp4') meta = reader.get_meta_data() meta ``` ``` {'plugin': 'ffmpeg', 'nframes': inf, 'ffmpeg_version': '4.2.2 built with gcc 9.2.1 (GCC) 20200122', 'codec': 'h264', 'pix_fmt': 'yuv444p', 'audio_codec':...

Why the mini-batch size are always set as 218 or 512, with the train-data size can't be evenly divisible by the input size? Thanks

__call__() keywords must be strings

1

When I run ```r %%R -i adata_luminals adata_luminals ``` in Jupyter, I have the error: ```pytb --------------------------------------------------------------------------- TypeError Traceback (most recent call last) in ----> 1 get_ipython().run_cell_magic('R', '-i adata_luminals', 'adata_luminals\n')...

Hello, I am not sure how can I get the `.bed` file for `TOBIAS ATACorrect -p` Should I use a peak file of a single sample or should I merge...

Hello: Can you please let me know what is the reason of this error? Thanks ``` clf = doubletdetection.BoostClassifier( n_iters=10, clustering_algorithm="louvain", standard_scaling=True, pseudocount=0.1, n_jobs=-1, ) doublets = clf.fit(adata.X).predict(p_thresh=1e-16, voter_thresh=0.5) doublet_score...

Code in Chapter 20 Clustering has redundant line #57

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Hello, The code in Chapter 20 Clustering has redundant line 57 https://github.com/joelgrus/data-science-from-scratch/blob/master/scratch/clustering.py ``` self.means = cluster_means(self.k, inputs, assignments) ``` This line is repeated with line 47 and can be deleted....

Thanks for the excellent book! Could you please let me know what is wrong with my code? Thanks. ``` x